docs: def _samtools_depths_at_known_snps_all_wild(sequence_meta, contig_name, cluster, variant_list):
      '''Input is a known variants, as sequence_metadata object. The
         assumption is that both the reference and the assembly have the
         variant type, not wild type. The list variant_list should be a list
         of pymummer.variant.Variant objects, only contaning variants to the
         relevant query contig'''
      ref_nuc_range = sequence_meta.variant.nucleotide_range()
  
      if ref_nuc_range is None:
          return None
  
      bases = []
      ctg_nts = []
      ref_nts = []
      smtls_total_depths = []
      smtls_nts = []
      smtls_depths = []
      contig_positions = []
  
      for ref_position in range(ref_nuc_range[0], ref_nuc_range[1]+1, 1):
          nucmer_match = cluster.assembly_compare.nucmer_hit_containing_reference_position(cluster.assembly_compare.nucmer_hits, cluster.ref_sequence.id, ref_position, qry_name=contig_name)
  
          if nucmer_match is not None:
              # work out contig position. Needs indels variants to correct the position
              ref_nts.append(cluster.ref_sequence[ref_position])
              contig_position, in_indel = nucmer_match.qry_coords_from_ref_coord(ref_position, variant_list)
              contig_positions.append(contig_position)
              bases, total_depth, base_depths = cluster.samtools_vars.get_depths_at_position(contig_name, contig_position)
              ctg_nts.append(cluster.assembly.sequences[contig_name][contig_position])
              smtls_nts.append(bases)
              smtls_total_depths.append(total_depth)
              smtls_depths.append(base_depths)
  
      ctg_nts = ';'.join(ctg_nts) if len(ctg_nts) else '.'
      ref_nts = ';'.join(ref_nts) if len(ref_nts) else '.'
      smtls_nts = ';'.join(smtls_nts) if len(smtls_nts) else '.'
      smtls_total_depths = ';'.join([str(x)for x in smtls_total_depths]) if len(smtls_total_depths) else '.'
      smtls_depths = ';'.join([str(x)for x in smtls_depths]) if len(smtls_depths) else '.'
      ctg_start = str(min(contig_positions) + 1) if contig_positions is not None else '.'
      ctg_end = str(max(contig_positions) + 1) if contig_positions is not None else '.'
  
      return [str(x) for x in [
          ref_nuc_range[0] + 1,
          ref_nuc_range[1] + 1,
          ref_nts,
          ctg_start,
          ctg_end,
          ctg_nts,
          smtls_total_depths,
          smtls_nts,
          smtls_depths
      ]]